LXL04_011401 | RubberDandelionOmics

Gene overview

LXL04_011401

Reference: OH-1004 Chr: Chr02 Coordinates: 163834866-163835950 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1020 bp · LXL04_011401|LXL04_011401|OH1004|cDNA

ATGGCCGAAAGAACAAAGAATGAGATGGAGAATTTGTCTCTACAGACGAAGAACAGGTTTTCGAGAGATTTATTGCAGAGATTTATGGTGAATAGTACCAATTTAGGAGATCCGAGAGGATCCGACCCGGAAGATGAAGTAGAGTTGAATCTCGGATTGTCGTTAGGTGGACGATTTGGCGTGGACAAAAGTAATAGCTCGTTGGTGAGGTCGTCTTCCATTGCTGCGATTTTGCCTGTGGTAAAGGACGACGACGTTTT...

CDS

Download CDS FASTA

1020 bp · LXL04_011401|LXL04_011401|OH1004|CDS

ATGGCCGAAAGAACAAAGAATGAGATGGAGAATTTGTCTCTACAGACGAAGAACAGGTTTTCGAGAGATTTATTGCAGAGATTTATGGTGAATAGTACCAATTTAGGAGATCCGAGAGGATCCGACCCGGAAGATGAAGTAGAGTTGAATCTCGGATTGTCGTTAGGTGGACGATTTGGCGTGGACAAAAGTAATAGCTCGTTGGTGAGGTCGTCTTCCATTGCTGCGATTTTGCCTGTGGTAAAGGACGACGACGTTTT...

Protein

Download Protein FASTA

339 aa · LXL04_011401|LXL04_011401|OH1004|PROTEIN

MAERTKNEMENLSLQTKNRFSRDLLQRFMVNSTNLGDPRGSDPEDEVELNLGLSLGGRFGVDKSNSSLVRSSSIAAILPVVKDDDVLGVRQRETGHGIGGPAYSSLIRTASLPLESEEWRKRKELQSLKRLAAKRRRSEKQRNLPKVEKEQHVAAKGRVGSSVGPSLGSGNWDFNVATATLTSDGNVGGLTPPVESQTSIKSEFESRQLQGSINEAEATKPASMQQSGQERSSEGGSSSSRSKMADRPPALRLSRPKTGK...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_011401`
TK1151 ID	TkA02G610630
OH-1004 ID	LXL04_011401
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011401

Location Chr02:163834866-163835950 (+)

Description Similar to AFP1: Ninja-family protein AFP1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g69260`	Acts as a negative regulator of abscisic acid (ABA) response during germination through the ubiquitin-mediated proteolysis of ABI5/DPBF1.	No verified direct reference in this release
`At1g13740`	Acts as a negative regulator of abscisic acid (ABA) response during germination through the ubiquitin-mediated proteolysis of ABI5/DPBF1.	A small plant-specific protein family of ABI five binding proteins (AFPs) regulates stress response in germinating Arabidopsis seeds and seedlings.2008 · DOI: 10.1007/s11103-008-9344-2
`At3g29575`	Acts as a negative regulator of abscisic acid (ABA) response and stress responses.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011401 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007165 signal transduction Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G13740

ath:AT1G69260

ath:AT3G29575

zma:100280792

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.977

Rank 1 · LXL04_011401 · OH-1004

Cytoplasm0.083

Rank 2 · LXL04_011401 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_011401 · OH-1004

Endoplasmic reticulum0.015

Rank 4 · LXL04_011401 · OH-1004

Plastid0.012

Rank 5 · LXL04_011401 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF07897.17EAR44-76 aa

PF16136.11NLS_NINJA_AFP106-141 aa

PF16135.11TDBD297-331 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011401	`PF07897.17`	EAR	44	76	1.3e-16	60.6
LXL04_011401	`PF16136.11`	NLS_NINJA_AFP	106	141	7.5e-17	61.5
LXL04_011401	`PF16135.11`	TDBD	297	331	3.2e-09	37.4

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9LQ98`	Arabidopsis thaliana	Ninja-family protein AFP1	44.807%	Swiss-Prot	moderate database homology
`Q9LMX5`	Arabidopsis thaliana	Ninja-family protein AFP2	40.496%	Swiss-Prot	moderate database homology
`Q94F39`	Arabidopsis thaliana	Ninja-family protein AFP3	43.098%	Swiss-Prot	moderate database homology

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